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poolSwap.py
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poolSwap.py
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def mean(listA):
m = float(sum(listA)) / float(len(listA))
return m
def stdev(listA):
import math
m = mean(listA)
difs = [x-m for x in listA]
sqdifs = [d*d for d in difs]
ssd = sum(sqdifs)
var = ssd / (len(listA)-1)
stdev = math.sqrt(var)
return stdev
def getToSwap(index1,index2,clusterDict,swap):
import copy
dup = copy.deepcopy(clusterDict)
index1KEY = []
index2KEY = []
index1VAL = []
index2VAL = []
for j in dup:
#print
#print j,":",
i = dup[j][2] ##gets barcode
#print i,"i"
if i == index1:
index1KEY.append(j)
index1VAL.append(dup[j])
#print index1KEY,index1VAL,"index1"
if i == index2:
index2KEY.append(j)
index2VAL.append(dup[j])
#print index2KEY,index2VAL,"index2"
#print
index1KEY.sort()
index2KEY.sort()
return index1KEY,index2KEY,index1VAL,index2VAL
def swapFunction(keys1,keys2,vals1,vals2,clusterDict,swap):
import copy
dup = copy.deepcopy(swap)
org = copy.deepcopy(clusterDict)
#print "copied"
#print keys1,"keys1"
#print keys2,"keys2"
#print "----"
for i in range(len(keys1)):
#print i,"i:"
#print "before",keys1[i],dup[keys1[i]],keys2[i],dup[keys2[i]]
tempswap1 = org[keys1[i]]
tempswap2 = org[keys2[i]]
#print "before",tempswap1,tempswap2
tempswap1[0],tempswap2[0] = tempswap2[0],tempswap1[0]
tempswap1[2],tempswap2[2] = tempswap2[2],tempswap1[2] ## successfully changing
#print "after",tempswap1,tempswap2
dup[keys1[i]] = tempswap1
dup[keys2[i]] = tempswap2
#print "after",keys1[i],dup[keys1[i]],keys2[i],dup[keys2[i]]
#print
#print "END SWAP FUNCTION ----------------------------------------------@@"
return dup
def getPerms(indexList):
from itertools import permutations
permuteList = []
first = True
for i in permutations(indexList,len(indexList)):
if first == True:
original = i
first = False
permuteList.append(i)
return permuteList
def getDesAvgSD(clusterDict):
son = []
chi = []
out = []
for i in clusterDict:
desert = clusterDict[i][-1]
clust = clusterDict[i][0]
if desert == "Son":
son.append(clust)
elif desert == "Chi":
chi.append(clust)
elif desert == "Out":
out.append(clust)
else:
print "error"
meanSon = mean(son)
sdSon = stdev(son)
meanChi = mean(chi)
sdChi = stdev(chi)
meanOut = mean(out)
sdOut = stdev(out)
return [meanSon,sdSon],[meanChi,sdChi],[meanOut,sdOut]
def swapList(list1,list2,clusterDict,swap):
import copy
#print "list1",list1
#print "list2",list2
if len(list1) != len(list2):
print "ERROR"
return []
dup = copy.deepcopy(swap)
org = copy.deepcopy(clusterDict)
#print "original dict"
#print org
#print
swappedList = []
swappedPairs = []
for i in range(len(list1)):
#print "I",i
if list1[i] != list2[i] and list1[i]:
A,B = list1[i],list2[i]
#print "A",A,"B",B
#if A not in swappedList and B not in swappedList:
if [A,B] not in swappedPairs:
#swappedList.append(A)
#swappedList.append(B)
swappedPairs.append([A,B])
#swappedPairs.append([B,A])
#print swappedPairs,"swapped"
keys1,keys2,vals1,vals2 = getToSwap(A,B,org,dup) ## GET TO SWAP
#print keys1,keys2,vals1,vals2, "LISTI"
#print
dup = swapFunction(keys1,keys2,vals1,vals2,org,dup) ## SWAP FUNCTION
#print "DUP",dup
#print dup == org
#else:
#print "already swapped"
#print "done"
if dup == clusterDict:
print "\tERROR, NO SWAP--------------------------"
return dup,swappedPairs
def compareDictMSD(orgDict,dict2):
son1,chi1,out1 = getDesAvgSD(orgDict)
son2,chi2,out2 = getDesAvgSD(dict2)
sonDevDif = son1[1] - son2[1] ## if positive, permutation is better
chiDevDif = chi1[1] - chi2[1]
outDevDif = out1[1] - out2[1]
#print sonDevDif,chiDevDif,outDevDif
sumSD = sum([sonDevDif,chiDevDif,outDevDif])
return sumSD,son2,chi2,out2 ## returns the sum SD dif and the means of the new cluster
def allDictPermutations(clusterDict,indexList,outfile):
import copy
swap = copy.deepcopy(clusterDict)
print >>outfile, "original list:","\t",indexList
permuteList = getPerms(indexList)
permLen = len(permuteList)
#print permLen,"PERMLEN"
print >>outfile, "num permutations:","\t",permLen
print >>outfile, "NEW PERMUTATION","\t","PAIRS SWAPPED","\t","SUM DIF IN SD","\t","SON MEAN/SD","\t","CHI MEAN/SD","\t","OUT MEAN/SD"
for permTUP in permuteList:
perm = list(permTUP)
#print perm,indexList,perm==indexList
if perm != indexList:
swappedDict,swappedPairs = swapList(perm,indexList,clusterDict,swap)
#print swappedDict,"\n",swappedPairs,"DICT/PAIRS"
sdDif,sonM,chiM,outM = compareDictMSD(clusterDict,swappedDict)
#print sdDif
print >>outfile, perm,"\t",swappedPairs,"\t",sdDif,"\t",sonM,"\t",chiM,"\t",outM,"\t",
for i in ["P1_P1F_01","P1_P1F_2","P1_P1F_3","P1_P1F_4","P1_P1F_5","P1_P1F_6","P1_P1F_15","P1_P1F_16"]:
print >>outfile,swappedDict[i][2],
print >>outfile, "\n",
else:
sdDif,sonM,chiM,outM = compareDictMSD(clusterDict,clusterDict)
print >>outfile, perm,"\t","NONE","\t",sdDif,"\t",sonM,"\t",chiM,"\t",outM
## print "ARE SWAP AND CLUST EQUAL?"
## print swappedDict == clusterDict
## for key in swappedDict:
## print key, swappedDict[key],clusterDict[key]
if __name__ == "__main__":
#import csv
## read file
poolfile = open("C:/Users/Kaiya/Dropbox/Docs For Brian/THESIS/Raw Specimen Data/QUALITY_CHECK_testCSV.csv","rU")
#poolfile = open("C:/Users/Kaiya/Dropbox/Docs For Brian/THESIS/Raw Specimen Data/QUALITY_CHECK_CSV.csv","rU")
lines = poolfile.readlines()
poolfile.close()
clusterDict = {}
for i in lines:
k1,loc,iden,pool,barcode,des = i.strip().split(",")
#print k1
if k1 != "K1AVG":
clusterDict[iden] = [float(k1),pool,int(barcode),des[0:3]]
indexList = [1,2,3,4,5,6,15,16]
## #perm = [4,6,3,2,16,5,1,15]
## perm = [16,15,6,5,4,3,2,1]
##
## a,b,c,d = getToSwap(1,4,clusterDict)
## print a,"\n"
## print b,"\n"
## print c,"\n"
## print d,"\n"
## print "--------------------"
##
## e = swapFunction2(a,b,clusterDict)
#outfile = open("C:/Users/Kaiya/Dropbox/Docs For Brian/THESIS/Raw Specimen Data/QUALITY_CHECK_PERMSD.csv","w")
outfile = open("C:/Users/Kaiya/Dropbox/Docs For Brian/THESIS/Raw Specimen Data/QUALITY_CHECK_PERMSD_test.csv","w")
allDictPermutations(clusterDict,indexList,outfile)
outfile.close()